CAPN9 p.Ala101=
c.303C>T · rs150220094 · VCV2640069
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0454%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -14 | GERP -4.9 |
| Overall | ||
| CADD | 0.167 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0454%
European (non-Finnish) · 535/1,178,034 alleles
Filtering AF
0.0422%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0409%
Overall
0.0354%
570/1,608,632 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0454% | 2,202 |
| Remaining individualsnot grpmax-eligible | 0.0177% | 5,664 |
| South Asian | 0.0112% | 8,964 |
| Finnishnot grpmax-eligible | 0.0109% | 9,144 |
| Admixed American | 0.00677% | 14,772 |
| African / African-American | 0.00402% | 24,869 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- CAPN9
- Protein
- p.Ala101=
- Coding
- c.303C>T
- MANE Select
- NM_006615
- dbSNP
- rs150220094
- Type
- single nucleotide variant
- Location
- chr1:230759531 (GRCh38)
- Gene constraint
- LOEUF 1.036 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 90.14 · 2 PDB
- Residue 101
- the calpain catalytic domain; an α-helix
Similar variants
- CAPN9 c.1657+2T>G Uncertain significance ★ same type
- CAPN9 p.Ala255Thr Uncertain significance ★ ⚠ same type
- CAPN9 p.Ala345Val Uncertain significance ★ ⚠ same type
- CAPN9 p.Ala525Asp Uncertain significance ★ ⚠ same type
- CAPN9 p.Ala531Thr Uncertain significance ★ same type
- CAPN9 p.Ala605Thr Uncertain significance ★ ⚠ same type
- CAPN9 p.Arg115Gly Uncertain significance ★ ⚠ same type
- CAPN9 p.Arg149His Uncertain significance ★ ⚠ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/capn9-p-ala101 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown